{"id":31065023,"url":"https://github.com/gersteinlab/brainpgene","last_synced_at":"2025-09-15T15:44:10.736Z","repository":{"id":310570007,"uuid":"1040380908","full_name":"gersteinlab/brainPgene","owner":"gersteinlab","description":null,"archived":false,"fork":false,"pushed_at":"2025-08-18T22:58:36.000Z","size":55,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-08-19T00:25:28.707Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/gersteinlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-08-18T22:26:17.000Z","updated_at":"2025-08-18T22:58:39.000Z","dependencies_parsed_at":"2025-08-19T00:37:24.200Z","dependency_job_id":null,"html_url":"https://github.com/gersteinlab/brainPgene","commit_stats":null,"previous_names":["gersteinlab/brainpgene"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/gersteinlab/brainPgene","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FbrainPgene","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FbrainPgene/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FbrainPgene/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FbrainPgene/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gersteinlab","download_url":"https://codeload.github.com/gersteinlab/brainPgene/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FbrainPgene/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275281955,"owners_count":25437090,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-15T02:00:09.272Z","response_time":75,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-09-15T15:44:06.821Z","updated_at":"2025-09-15T15:44:10.728Z","avatar_url":"https://github.com/gersteinlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Comprehensive analysis of pseudogene expression in human and macaque brains compared to other tissues\n\n## Overview\nPseudogenes are DNA sequences similar to protein-coding genes that contain disabling mutations rendering them unable to produce fully functional proteins. Traditionally, pseudogenes have been considered non-functional genomic elements that evolve under neutral selection, permitting the accumulation of deleterious mutations such as in-frame stop codons and frameshift insertions or deletions. \n\nIn this study, we aim to explore whether pseudogenes could possess putative biological relevance in the brain. To that end, we propose three primary objectives:\n- characterizing the tissue- and brain region-specificity of pseudogene expression;\n- identifying temporally dynamic pseudogenes across diverse brain regions;\n- identifying differentially expressed pseudogenes associated with psychiatric disorders.\n\n## Dataset\n**PsychENCODE Consortium (PEC)**\n- [Spatiotemporal transcriptomic divergence across human and macaque brain development](https://www.science.org/doi/10.1126/science.aat8077) (Zhu et al., *Science*, 2018).\n- [Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder](https://www.science.org/doi/10.1126/science.aat8127) (Gandal et al., *Science*, 2018)\n\n**ENCODE EN-TEx**\n- [The EN-TEx resource of multi-tissue personal epigenomes \u0026 variant-impact models](https://www.cell.com/cell/fulltext/S0092-8674(23)00161-7) (Rozowsky et al., *Cell*, 2023)\n\nThe publicly available RNA-seq reads used in this study were downloaded as BAM files from [Synapse](https://www.synapse.org/). \n\nThe expression data of the pseudogenes and protein-coding genes in human and macaque quantified based on the computational framework in this study were deposited to [Zenodo](https://doi.org/10.5281/zenodo.16810204).\n\n\n## For more information\n\nIf you have additional questions, please contact [Yunzhe Jiang](mailto:yunzhe.jiang@yale.edu) and [Yucheng T. Yang](mailto:yangyc2016@gmail.com).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgersteinlab%2Fbrainpgene","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgersteinlab%2Fbrainpgene","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgersteinlab%2Fbrainpgene/lists"}